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Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K1E PDB ENTRY 1K1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 30% w/v polyethelene glycol (PEG) 4,000, 0.1 M Tris HCl pH 8.5, 0.2 M sodium acetate and 10 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.23 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.958 α = 90 b = 106.602 β = 90 c = 74.83 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2005-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.629 50 98.4 0.046 35.4 12.2 81247 2 2 27.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.629 1.69 91.2 0.508 2.4 6.6 7434
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FREE R PDB ENTRY 1K1E 1.629 49.061 1.89 81192 7786 98.22 0.176 0.174 0.1611 0.207 0.1954 RANDOM 32.003
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -6.861 -5.993 0.94
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.919 f_angle_d 1.12 f_chiral_restr 0.073 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5180 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms 170
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction CrystalClear data collection MOLREP phasing